Combinatorial analysis of interacting RNA molecules

DOI10.1016/J.MBS.2011.04.009MaRDI QIDQ648014zbMATH OpenOpenAlexWikidataFDO

Authors Thomas J. X. Li, Christian M. Reidys

Publication date 22 November 2011

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1006.4089

zbMATH Keywords

shapesingularity analysisRNA interactionRNA secondary structurejoint structuresymbolic enumeration

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Symbolic computation and algebraic computation (68W30) Computational methods for problems pertaining to biology (92-08)

Abstract: Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.

Recommendations

• Combinatorics of RNA-RNA interaction
• A combinatorial approach for multiple RNA interaction: formulations, approximations, and heuristics
• Research in Computational Molecular Biology
• Publication:4731051
• Counting RNA pseudoknotted structures (extended abstract)

Cites work

• scientific article; zbMATH DE number 1268810 (Why is no real title available?)
• AN EXAMPLE IN THE THEORY OF THE SPECTRUM OF A FUNCTION
• Combinatorial design of pseudoknot RNA
• Combinatorics of RNA secondary structures
• Combinatorics of RNA-RNA interaction
• Linear trees and RNA secondary structure
• Modular, \(k\)-noncrossing diagrams
• RNA secondary structure: a complete mathematical analysis
• Research in Computational Molecular Biology
• Thermodynamic Analysis of Interacting Nucleic Acid Strands

Cited in

(15)

• Parametric analysis of RNA branching configurations
• Making multiple RNA interaction practical
• Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions
• Research in Computational Molecular Biology
• A grammatical approach to RNA-RNA interaction prediction
• Statistics of topological RNA structures
• NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES
• Combinatorics of RNA-RNA interaction
• Asymptotic number of hairpins of saturated RNA secondary structures
• Thermodynamic Analysis of Interacting Nucleic Acid Strands
• Automated prediction of three-way junction topological families in RNA secondary structures
• Symmetric circular matchings and RNA folding
• Using temperature effects to predict the interactions between two RNAs
• The block spectrum of RNA pseudoknot structures
• Fatgraph models of RNA structure

This page was built for publication: Combinatorial analysis of interacting RNA molecules

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q648014)